[English] 日本語
Yorodumi
- PDB-6bll: Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6bll
TitleCryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution
DescriptorCleavage and polyadenylation specificity factor subunit 1
pre-mRNA 3' end processing protein WDR33
Cleavage and polyadenylation specificity factor subunit 4/RNA Complex
KeywordsRNA BINDING PROTEIN/RNA / Recognition of the AAUAAA polyadenylation signal (PAS) / Hoogsteen base pair / zinc finger / RNA BINDING PROTEIN-RNA complex
Specimen sourceHomo sapiens / human
Simian virus 40 / virus / SV40
MethodElectron microscopy (3.4 Å resolution / Particle / Single particle)
AuthorsSun, Y. / Zhang, Y. / Hamilton, K. / Walz, T. / Tong, L.
CitationProc. Natl. Acad. Sci. U.S.A., 2017

Proc. Natl. Acad. Sci. U.S.A., 2017 Yorodumi Papers
Molecular basis for the recognition of the human AAUAAA polyadenylation signal.
Yadong Sun / Yixiao Zhang / Keith Hamilton / James L Manley / Yongsheng Shi / Thomas Walz / Liang Tong

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 1
B: pre-mRNA 3' end processing protein WDR33
C: Cleavage and polyadenylation specificity factor subunit 4
E: RNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,8257
Polyers261,6284
Non-polymers1963
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)15890
ΔGint (kcal/M)-137
Surface area (Å2)64180

-
Components

#1: Polypeptide(L)Cleavage and polyadenylation specificity factor subunit 1 / Cleavage and polyadenylation specificity factor 160 kDa subunit / CPSF 160 kDa subunit


Mass: 161074.234 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q10570
#2: Polypeptide(L)pre-mRNA 3' end processing protein WDR33 / WD repeat-containing protein 33 / WD repeat-containing protein WDC146


Mass: 67546.812 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q9C0J8
#3: Polypeptide(L)Cleavage and polyadenylation specificity factor subunit 4 / CPSF30 / Cleavage and polyadenylation specificity factor 30 kDa subunit / CPSF 30 kDa subunit / NS1 effector domain-binding protein 1 / Neb-1 / No arches homolog


Mass: 27646.055 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: O95639
#4: RNA chainRNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3')


Mass: 5361.317 Da / Num. of mol.: 1 / Source: (synth.) Simian virus 40 / virus / SV40
#5: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Quaternary complex of human CPSF-160-WDR33-CPSF-30 with AAUAAA polyadenylation signalCOMPLEX1, 2, 3, 40MULTIPLE SOURCES
2CPSF-160-WDR33COMPLEX1, 21RECOMBINANT
3CPSF-30COMPLEX31RECOMBINANT
4AAUAAA polyadenylation signalCOMPLEX41NATURAL
Molecular weight
IDValueUnitsEntity assembly IDExperimental value
10.255MEGADALTONS1YES
20.225MEGADALTONS2
30.027MEGADALTONS3
40.005MEGADALTONS4
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens
239606Homo sapiens
3410633Simian virus 40
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
127111Trichoplusia ni
23562Escherichia coli
Buffer solutionDetails: 25 mM Tris-HCl, pH 7.9, 380 mM NaCl, 5 mM DTT / pH: 7.9
Buffer componentConc.: 0.38 mg/ml / Units: mM / Name: sodium chloride / Formula: NaCl
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 225000 / Calibrated magnification: 46729 / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 2800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2468
Image scansMovie frames/image: 40 / Used frames/image: 1-40

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategoryImage processing IDFitting ID
1GautomatchPARTICLE SELECTION1
4CTFFINDCTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
9PHENIXMODEL REFINEMENT1
13RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1144122
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 173632 / Symmetry type: POINT
Atomic model buildingPDB-ID: 2RHK
Pdb chain ID: C / Pdb chain residue range: 56-116
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01013775
ELECTRON MICROSCOPYf_angle_d1.02018701
ELECTRON MICROSCOPYf_dihedral_angle_d8.1518188
ELECTRON MICROSCOPYf_chiral_restr0.0602078
ELECTRON MICROSCOPYf_plane_restr0.0082361

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more